The overall goal of the Molecular Aspects of Drug Design Section is to discover new agents, and approaches to the development of new agents against cancer and viral diseases. This goal is accomplished through an interdisciplinary combination of chemistry and biology that involves critical collaborations in basic and translational research. We had previously described compounds of that are bifunctional DNA-interacting compounds, the bisimidazoacridones, that inhibit the growth of tumors, especially of the GI tract. These compounds interact with DNA by a combination of intercalation and minor groove binding and appear to function by capturing a critical protein that is involved in DNA repair or transcription. When the compounds are symmetrical their biological effect is to arrest cell growth at specific checkpoints of the cell cycle. In some instances, compounds of this class are extremely potent anti-HIV agents, where they selectively inhibit the transcription of the viral genome. In contrast, some unsymmetrical bifunctional agents, such as those that contain an imidazoacridone moiety on one end of a linker and a naphthylimide moiety on the other, are potently cytotoxic but still exhibit high selectivity. These compounds bind to DNA through the major groove and these complexes then also interact with nuclear proteins involved in DNA repair and transcription. For example, topoisomerase I is a target, although not a critical one. One of these agents HKH40A, is toxic in the nanomolar range to various GI cancers, including those of the colon, pancreas and liver and exhibits outstanding in vivo activity. Continuing mechanistic studies in our laboratory and also in those of our collaborators have revealed that while HKH40A has several molecular targets, the principal mode of action appears to be transcriptional down-regulation of genes responsible for initiation and maintenance of DNA replication. Critical genes that are down-regulated by HKH40A include ribonucleotide reductase that is responsible for maintaining dNTP pools, as well as critical replication kinases Cdc6 and Cdc7. This inhibition results in up-regulation of the p53-dependent apoptotic cascade in p53 (+/+) tumors, while in p53 (-/-) tumors HKH40A causes premature entry into S phase that results in genomic instability and death. Normal cells are protected from the lethal effects of the drug by correctly functioning checkpoint controls that are frequently disrupted in cancer. HKH40A is in clinical development in collaboration with a commercial partner. Some G-protein coupled receptors (GPCR) are over-expressed in tumors. We had previously demonstrated that natural ligands for these receptors can be substantially modified in certain instances without loss of binding affinity or their ability to be internalized. We have shown that synthetic ligands that consist of the receptor recognition sequence, a linker that can be cleaved by intracellular proteases and a highly toxic moiety can be used to specifically target the tumor cells that over-express the receptor. We have focused most of our attention on cholecystokinin 2 (gastrin) receptor (CCK2r) that is frequently over-expressed in GI tumors and on vasoactive intestinal peptide receptor (VIP) that is over-expressed in some lung cancers and in breast cancer. While we have been able to delineate the requirements for a successful GPCR targeted drug, the highly specific requirements for the linker and the toxic moiety have continued to present a significant research and development challenge. We have now overcome many of the difficulties that centered on the correct processing of the drug once it was internalized in cancer cells. We had shown earlier that properly designed synthetic peptides that correspond in sequence to native trans-membrane domains of polytopic membrane proteins can disrupt the function of the proteins, presumably by disrupting the assembly of the multi-helix trans-membrane bundles. Thus, proteins such as the G-protein coupled chemokine receptor CXCR4, which is critical for HIV entry into T-cells, and is also involved in metastatic spread of tumors as well their angiogenesis, can be inhibited at low nanomolar concentration with essentially absolute selectivity. We have applied this novel paradigm to design specific and highly active inhibitors of other GPCRs as well as inhibitors of ABC transporters, such as P-gp and ABCG2, that are involved in multi-drug resistance of many tumors. In collaborative research we have shown that this strategy can be used for the design of anti-tumor agents of great specificity in vivo. This approach allows the design of highly effective and specific inhibitors based solely on the knowledge of the primary sequence of a protein. Because the peptides interact well with only the target proteins, we have not found any significant treatment-related toxicity. In a collaborative effort with Dr. Susan Keay of the University of Maryland Medical School, we identified and carried out the total synthesis of the anti-proliferative factor, APF, which she isolated in minute quantities (< 1&#956;g) from the bladder epithelium of patients suffering from interstitial cystitis (IC), a debilitating bladder disease. APF is a small glycopeptide of unusual structure, where the nonapeptide sequence is 100% homologous with the 6th trans-membrane domain of the frizzled 8 gene, while the sugar moiety is a sialylated Tf.(Gal-1,3-GalNHAc) antigen. We have carried out extensive structure/activity studies on the molecule, the results of which have allowed us to identify the critical elements that define the extremely potent epithelial cell growth inhibition chartacteristics of APF. The likely molecular receptor for APF has been identified in a further collaboration with Dr. Keay as well as Drs. Veenstra and Conrads of the Laboratory of Proteomics and Analytical Technologies, SAIC-Frederick. Additional collaborative studies with Dr Keay have resulted in production of antibodies to APF, which have allowed her to detect IC from urine of patients, an important diagnostic advance, which is being developed in collaboration with an industrial partner. In a very exciting development, APF and several of its synthetic analogs have been found to be potent inhibitors of renal and bladder cancers. Collaboration with Dr. Brian Carr of the Starzl Transplantation Center of the University of Pittsburgh led to the discovery of a new class of highly selective inhibitors of dual specificity phosphatases based on the N-aryl maleimide nucleus. The the lead compound from this series, PM20, is a highly selective inhibitor of Cdc25A, with some reactivity toward the Cdc25B isoform. The compound causes dramatic up-regulation of phosphorylated ERK1/2 but not of the other MAPkinases such as p38 and JNK. The cyclin-dependent kinases Cdk2 and Cdk4, which are substrates for Cdc25A, were found to be hyper-phosphorylated in the presence of PM20 also shown The drug was found to be potently active against orthotopic hepatocellular carcinoma in the rat with verylittle evidence of toxicity